private void AddCEMzSteps(int start, int count)
{
int step = count / 2;
for (int i = count - 1; i >= 0; i--)
{
var chromId = _chromIds[start + i];
var chromKeyNew = chromId.Key.ChangeOptimizationStep(step);
_chromIds[start + i] = new ChromKeyProviderIdPair(chromKeyNew, chromId.ProviderId);
step--;
}
}
public ChromatogramDataProvider(MsDataFileImpl dataFile,
ChromFileInfo fileInfo,
IProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_dataFile = dataFile;
if (_dataFile.IsThermoFile)
{
_readMaxMinutes = 4;
}
int len = dataFile.ChromatogramCount;
_chromIndices = new int[len];
bool fixCEOptForShimadzu = dataFile.IsShimadzuFile;
int indexPrecursor = -1;
var lastPrecursor = SignedMz.ZERO;
for (int i = 0; i < len; i++)
{
int index;
string id = dataFile.GetChromatogramId(i, out index);
if (!ChromKey.IsKeyId(id))
{
continue;
}
var chromKey = ChromKey.FromId(id, fixCEOptForShimadzu);
if (chromKey.Precursor != lastPrecursor)
{
lastPrecursor = chromKey.Precursor;
indexPrecursor++;
}
var ki = new ChromKeyProviderIdPair(chromKey, index);
_chromIndices[index] = indexPrecursor;
_chromIds.Add(ki);
}
// Shimadzu can't do the necessary product m/z stepping for itself.
// So, they provide the CE values in their IDs and we need to adjust
// product m/z values for them to support CE optimization.
if (fixCEOptForShimadzu)
{
FixCEOptForShimadzu();
}
if (_chromIds.Count == 0)
{
throw new NoSrmDataException(FileInfo.FilePath);
}
// CONSIDER(kaipot): Some way to support mzML files converted from MIDAS wiff files
_hasMidasSpectra = (dataFile.IsABFile) && SpectraChromDataProvider.HasSpectrumData(dataFile);
SetPercentComplete(50);
}
public ChromatogramDataProvider(MsDataFileImpl dataFile,
ChromFileInfo fileInfo,
IProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_dataFile = dataFile;
_globalChromatogramExtractor = new GlobalChromatogramExtractor(dataFile);
if (_dataFile.IsThermoFile)
{
_readMaxMinutes = 4;
}
int len = dataFile.ChromatogramCount;
_chromIndices = new int[len];
bool fixCEOptForShimadzu = dataFile.IsShimadzuFile;
int indexPrecursor = -1;
var lastPrecursor = SignedMz.ZERO;
for (int i = 0; i < len; i++)
{
int index;
string id = dataFile.GetChromatogramId(i, out index);
if (!ChromKey.IsKeyId(id))
{
continue;
}
var chromKey = ChromKey.FromId(id, fixCEOptForShimadzu);
if (chromKey.Precursor != lastPrecursor)
{
lastPrecursor = chromKey.Precursor;
indexPrecursor++;
}
if (chromKey.Precursor.IsNegative)
{
_sourceHasNegativePolarityData = true;
}
else
{
_sourceHasPositivePolarityData = true;
}
var ki = new ChromKeyProviderIdPair(chromKey, index);
_chromIndices[index] = indexPrecursor;
_chromIds.Add(ki);
}
// Shimadzu can't do the necessary product m/z stepping for itself.
// So, they provide the CE values in their IDs and we need to adjust
// product m/z values for them to support CE optimization.
if (fixCEOptForShimadzu)
{
FixCEOptForShimadzu();
}
if (_chromIds.Count == 0)
{
throw new NoSrmDataException(FileInfo.FilePath);
}
// CONSIDER: TIC and BPC are not well defined for SRM and produced chromatograms with over 100,000 points in
// Agilent CE optimization data. So, keep them off for now.
// foreach (int globalIndex in _globalChromatogramExtractor.GlobalChromatogramIndexes)
// {
// _chromIndices[globalIndex] = globalIndex;
// _chromIds.Add(new ChromKeyProviderIdPair(ChromKey.FromId(_globalChromatogramExtractor.GetChromatogramId(globalIndex, out int indexId), false), globalIndex));
// }
foreach (var qcTracePair in _globalChromatogramExtractor.QcTraceByIndex)
{
_chromIndices[qcTracePair.Key] = qcTracePair.Key;
_chromIds.Add(new ChromKeyProviderIdPair(ChromKey.FromQcTrace(qcTracePair.Value), qcTracePair.Key));
}
// CONSIDER(kaipot): Some way to support mzML files converted from MIDAS wiff files
_hasMidasSpectra = (dataFile.IsABFile) && SpectraChromDataProvider.HasSpectrumData(dataFile);
_ionMobilityUnits = dataFile.IonMobilityUnits;
_hasIonMobilityCombined = dataFile.HasCombinedIonMobilitySpectra; // When true, data source provides IMS data in 3-array format, which affects spectrum ID format
SetPercentComplete(50);
}